[Chimera-users] Question on aligning one molecule to two other molecules

Doc Deldou docdeldou at gmail.com
Wed Nov 18 04:45:52 PST 2020

Dear Chimera team,

I am trying to perform a "manual" docking of a DNA molecule in a protein
structure using homology with proteins structures resolved with DNA. I know
that the first part of my protein (the recognition domain) is similar to
one structure and the other part (the cleavage domain) is similar to
another one. So I built a dsDNA with the recognition sequence of my target
protein and I first aligned it with the DNA of the similar recognition
structure using the phoshore groups, then I matched aligned my protein
structure to the protein part of the similar recognition structure. After
that I matched aligned my protein to the similar protein cleavage domain
bringing the DNA molecule with it. And now ideally I would like to align
the DNA part with the DNA of the similar cleavage domain but keep the first
recognition part of my DNA more or less at the same position. So I tried to
align another copy of my DNA to both DNA molecules but I don't think it is
possible. Do you have a trick or a command I could use to reach my goal?
I'm using Chimera X. Below is what I obtained, in green my target protein,
in purple the DNA I first aligned relatively to the DNA of my similar
recognition structure, in "pink" the DNA strand of the similar cleavage
structure with the bond to be cleaved in yellow, and the dsDNA with all the
colored nucleotides is the one I am trying to position in between the two
site with also the bond to be cleaved in yellow. I tried to rotate it and
translate it manually to have something in between but some DNA parts are
clashing with the protein part and I would like to have something the more
accurate possible.

[image: manualdocking.jpg]
Best regards,

Adèle Dramé-Maigné

  Docteur en Biochimie
    et Instagrammeuse

Blog: http://bit.ly/2zkiPWI
LinkedIn: http://bit.ly/2afmtEq
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